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Yorodumi- PDB-1ckm: STRUCTURE OF TWO DIFFERENT CONFORMATIONS OF MRNA CAPPING ENZYME I... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ckm | ||||||
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Title | STRUCTURE OF TWO DIFFERENT CONFORMATIONS OF MRNA CAPPING ENZYME IN COMPLEX WITH GTP | ||||||
Components | MRNA CAPPING ENZYME | ||||||
Keywords | CAPPING ENZYME / MRNA / NUCLEOTIDYLTRANSFERASE | ||||||
Function / homology | Function and homology information 7-methylguanosine mRNA capping / mRNA guanylyltransferase activity / mRNA guanylyltransferase / GTP binding / ATP binding Similarity search - Function | ||||||
Biological species | Paramecium bursaria Chlorella virus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR WITH A MERCURY DERIVATIVE OBTAINED BY SOAKING THE CRYSTAL FOR TWO HOURS IN 1 MM THIMEROSAL, A SELENOMETHIONINE DERIVATIVE / Resolution: 2.5 Å | ||||||
Authors | Hakansson, K. / Doherty, A.J. / Wigley, D.B. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 1997 Title: X-ray crystallography reveals a large conformational change during guanyl transfer by mRNA capping enzymes. Authors: Hakansson, K. / Doherty, A.J. / Shuman, S. / Wigley, D.B. #1: Journal: To be Published Title: Crystallization of the RNA Guanylyltransferase of Chlorella Virus Pbcv-1 Change During Guanyl Transfer by Mrna Capping Enzymes Authors: Doherty, A.J. / Hakansson, K. / Ho, C.K. / Shuman, S. / Wigley, D.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ckm.cif.gz | 147.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ckm.ent.gz | 116.7 KB | Display | PDB format |
PDBx/mmJSON format | 1ckm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ckm_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 1ckm_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 1ckm_validation.xml.gz | 29.6 KB | Display | |
Data in CIF | 1ckm_validation.cif.gz | 42.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ck/1ckm ftp://data.pdbj.org/pub/pdb/validation_reports/ck/1ckm | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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5 |
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Unit cell |
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Details | THE TWO MOLECULES IN THE ASYMMETRIC UNIT ARE IN DIFFERENT CONFORMATIONS. THE PROTEIN IS MONOMERIC AND THIS ENTRY MERELY REPRESENTS A CO-CRYSTAL OF THE ENZYME IN TWO DIFFERENT CONFORMATIONS. |
-Components
#1: Protein | Mass: 37884.992 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Paramecium bursaria Chlorella virus 1 / Genus: Chlorovirus / Production host: Escherichia coli (E. coli) / References: UniProt: Q84424, mRNA guanylyltransferase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.5 Å3/Da / Density % sol: 65 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7.5 Details: HANGING DROP VAPOR DIFFUSION. 10-15 MG/ML PROTEIN IN 50 MM TRIS-HCL, 0.5 M NACL, 10 MM MGCL2, 5MM GTP, 2 MM EDTA, 4 MM DTT, PH 7.5 WERE MIXED WITH AN EQUAL VOLUME OF AND EQUILIBRATED AGAINST ...Details: HANGING DROP VAPOR DIFFUSION. 10-15 MG/ML PROTEIN IN 50 MM TRIS-HCL, 0.5 M NACL, 10 MM MGCL2, 5MM GTP, 2 MM EDTA, 4 MM DTT, PH 7.5 WERE MIXED WITH AN EQUAL VOLUME OF AND EQUILIBRATED AGAINST 100 MM TRIS-HCL, 200 MM NACL, 200 MM AMMONIUM SULFATE 34% MEOPEG 5000, PH 7.5., vapor diffusion - hanging drop | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: unknown / Details: Doherty, A.J., (1996) Nucl. Acids Res., 24. 2281. | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.448 |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jul 1, 1996 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.448 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. obs: 36196 / % possible obs: 97.5 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 48.3 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 13.3 |
-Processing
Software |
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Refinement | Method to determine structure: MIR WITH A MERCURY DERIVATIVE OBTAINED BY SOAKING THE CRYSTAL FOR TWO HOURS IN 1 MM THIMEROSAL, A SELENOMETHIONINE DERIVATIVE Resolution: 2.5→10 Å / σ(F): 0
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Displacement parameters | Biso mean: 29.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→10 Å
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Refine LS restraints |
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Xplor file |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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